CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Carnac(20)		Pknots
MCC	0.587	>	0.514
Average MCC ± 95% Confidence Intervals	0.544 ± 0.084	<	0.573 ± 0.098
Sensitivity	0.388	<	0.467
Positive Predictive Value	0.894	>	0.572
Total TP	455	<	548
Total TN	177075	>	176626
Total FP	78	<	466
Total FP CONTRA	9	<	56
Total FP INCONS	45	<	354
Total FP COMP	24	<	56
Total FN	718	>	625
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Carnac(20) and Pknots. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for Carnac(20) and Pknots).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for Carnac(20) and Pknots).
Comparison of average Matthews Correlation Coefficients (MCCs) for Carnac(20) and Pknots. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for Carnac(20) and Pknots).

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Performance of Carnac(20) - scored higher in this pairwise comparison

1. Total counts & total scores for Carnac(20)

Total Base Pair Counts
Total TP	455
Total TN	177075
Total FP	78
Total FP CONTRA	9
Total FP INCONS	45
Total FP COMP	24
Total FN	718

Total Scores
MCC	0.587
Average MCC ± 95% Confidence Intervals	0.544 ± 0.084
Sensitivity	0.388
Positive Predictive Value	0.894
Nr of predictions	33

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2. Individual counts for Carnac(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.73	0.55	1.00	6	400	0	0	0	0	5
2L94_A	HIV_FE links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	20
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.32	0.10	1.00	2	4558	1	0	0	1	18
2XQD_Y	tRNA links to Rfam database...	0.79	0.63	1.00	17	2833	0	0	0	0	10
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.27	0.07	1.00	3	5148	0	0	0	0	39
3A2K_C	tRNA links to Rfam database...	0.78	0.61	1.00	17	2909	0	0	0	0	11
3AMU_B	tRNA links to Rfam database...	0.69	0.59	0.80	16	2983	6	0	4	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.28	0.89	16	7363	2	1	1	0	41
3GX2_A	SAM links to Rfam database...	0.57	0.33	1.00	13	4358	0	0	0	0	27
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZF_C	5S_rRNA links to Rfam database...	0.73	0.56	0.97	30	6872	1	0	1	0	24
3J20_0	tRNA links to Rfam database...	0.62	0.53	0.73	16	2828	7	0	6	1	14
3J20_1	tRNA links to Rfam database...	0.86	0.74	1.00	17	2909	0	0	0	0	6
3J2L_3	5S_rRNA links to Rfam database...	0.46	0.34	0.64	18	7847	11	0	10	1	35
3JYV_7	tRNA links to Rfam database...	0.68	0.50	0.94	16	2833	1	0	1	0	16
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	15	6308	10	1	4	5	12
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.44	0.20	1.00	9	7012	2	0	0	2	37
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3PDR_A	ykoK links to Rfam database...	0.62	0.40	0.97	29	12850	3	0	1	2	43
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.13	0.70	7	14186	3	1	2	0	45
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.53	1.00	26	6995	0	0	0	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.19	1.00	6	3480	0	0	0	0	26

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Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	548
Total TN	176626
Total FP	466
Total FP CONTRA	56
Total FP INCONS	354
Total FP COMP	56
Total FN	625

Total Scores
MCC	0.514
Average MCC ± 95% Confidence Intervals	0.573 ± 0.098
Sensitivity	0.467
Positive Predictive Value	0.572
Nr of predictions	33

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2. Individual counts for Pknots [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.23	0.25	0.22	5	4537	31	1	17	13	15
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.32	0.31	0.34	13	5113	25	1	24	0	29
3A2K_C	tRNA links to Rfam database...	0.45	0.43	0.48	12	2901	13	2	11	0	16
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3G4S_9	5S_rRNA links to Rfam database...	0.25	0.21	0.31	12	7342	27	0	27	0	45
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.55	16	4342	14	1	12	1	24
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	0	1	0	11
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.51	0.75	27	7839	12	0	9	3	26
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.18	0.21	0.16	7	12203	41	13	23	5	26
3JYX_3	5S_rRNA links to Rfam database...	0.34	0.37	0.31	10	6296	24	9	13	2	17
3LA5_A	Purine links to Rfam database...	0.80	0.65	1.00	22	2463	0	0	0	0	12
3NPB_A	SAM links to Rfam database...	0.76	0.67	0.86	31	6985	8	1	4	3	15
3O58_2	5S_rRNA links to Rfam database...	0.83	0.74	0.93	28	7230	3	0	2	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.27	0.31	0.24	11	12357	38	11	24	3	24
3PDR_A	ykoK links to Rfam database...	0.54	0.44	0.65	32	12831	19	0	17	2	40
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.07	0.08	0.07	4	14141	54	4	47	3	48
3ZEX_D	5S_rRNA links to Rfam database...	0.27	0.24	0.30	12	6981	28	0	28	0	37
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.48	0.38	0.63	12	3467	7	0	7	0	20

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Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.

Table of contents:

Overview

Performance plots

Performance of Carnac(20) - scored higher in this pairwise comparison

1. Total counts & total scores for Carnac(20)

2. Individual counts for Carnac(20) [ download as .csv ]

Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

2. Individual counts for Pknots [ download as .csv ]